Hi there,
You have to be a little bit careful with the Puppet tool. The Puppet tool adds a mesh to the Alpha channel of the layer and fixes that mesh on top of the image. Therefore, if the image's alpha changes shape (via animation or effects) then the mesh will no longer match the image.
Your solution would be to animate your character using the Puppet tool then precompose this character into a new comp. Make the new comp 3D and then do your thang with it as required. Don't collapse Transformations and don't collect $200 dollars when you pass go! ;-)
Also, if you want to make the characters eyes blink or do any other preliminary animation on the character before using the puppet tool, these must be done in a nested comp and they must not affect the Alpha "shape" of the layer.
Phew, hope that helped!
Here's a tutorial on the puppet tool that covers some of this;
http://www.angietaylor.co.uk/a-free-tutorial-gift-for-the-holidays/
cheers,
Angie
Angie Taylor animation & illustration for television, film, web and devices
http://www.angietaylor.co.uk
Twitter: theangietaylor
Linkedin: theangietaylor
http://www.facebook.com/pages/Angie-Taylor/118378194869002
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